On Wed, Jun 12, 2013 at 11:33 AM, <cieplak.cgl.ucsf.edu> wrote:
> There is nothing about solvateDontClip command in LeaP documentation.
>
True -- I hadn't known about it for this reason. It exists, nonetheless...
$ tleap
-I: Adding /Users/swails/amber/dat/leap/prep to search path.
-I: Adding /Users/swails/amber/dat/leap/lib to search path.
-I: Adding /Users/swails/amber/dat/leap/parm to search path.
-I: Adding /Users/swails/amber/dat/leap/cmd to search path.
Welcome to LEaP!
(no leaprc in search path)
> help solvateDontClip
solvateDontClip solute solvent buffer [ closeness ]
UNIT _solute_
UNIT _solvent_
object _buffer_
NUMBER _closeness_
This command is identical to the solvateBox command except that the
solvent box that is created is not clipped to the boundary of the
_buffer_ region. This command forms larger solvent boxes than does
solvateBox because it does not cause solvent that is outside the buffer
region to be discarded. This helps to preserve the periodic structure
of properly constructed solvent boxes, preventing hot-spots from
forming.
>
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jun 12 2013 - 09:30:04 PDT
